Automated protein identification by tandem mass spectrometry: Issues and strategies
Protein identification by tandem mass spectrometry (MS/MS) is key to most proteomics projects and has been widely explored in bioinformatics research. Obtaining good and trustful identification results has important implications for biological and clinical work. Although well matured, automated soft...
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Published in | Mass spectrometry reviews Vol. 25; no. 2; pp. 235 - 254 |
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Main Authors | , , |
Format | Journal Article |
Language | English |
Published |
Hoboken
Wiley Subscription Services, Inc., A Wiley Company
01.03.2006
Wiley |
Subjects | |
Online Access | Get full text |
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Summary: | Protein identification by tandem mass spectrometry (MS/MS) is key to most proteomics projects and has been widely explored in bioinformatics research. Obtaining good and trustful identification results has important implications for biological and clinical work. Although well matured, automated software identification of proteins from MS/MS data still faces a number of obstacles due to the complexity of the proteome or procedural issues of mass spectrometry data acquisition. Expected or unexpected modifications of the peptide sequences, polymorphisms, errors in databases, missed or non‐specific cleavages, unusual fragmentation patterns, and single MS/MS spectra of multiple peptides of the same m/z are so many pitfalls for identification algorithms. A lot of research work has been carried out in recent years that yielded new strategies to handle a number of these issues. Multiple MS/MS identification algorithms are now available or have been theoretically described. The difficulty resides in choosing the most adapted method for each type of spectra being identified. This review presents an overview of the state‐of‐the‐art bioinformatics approaches to the identification of proteins by MS/MS to help the reader doing the spadework of finding the right tools among the many possibilities offered. © 2005 Wiley Periodicals, Inc. Mass Spec Rev 25:235–254, 2006 |
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Bibliography: | istex:8E16ED9B3855D40A2C6F650087C934C203C5C731 ArticleID:MAS20068 ark:/67375/WNG-P599SJ7V-M ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-3 content type line 23 ObjectType-Review-1 |
ISSN: | 0277-7037 1098-2787 |
DOI: | 10.1002/mas.20068 |